RetrogeneDB ID: retro_pcap_389

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_65594:2707..2995(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: VAMP3
• Ensembl ID: ENSPCAG00000004825
• Aliases: None
• Description: vesicle-associated membrane protein 3 [Source:HGNC Symbol;Acc:12644]

Sequence

>retro_pcap_389
AGTTTGGCTGCGATCTCCTTTTCCAGGCTTATCTCTAGCAGTAATCAAAGACTGCAGCAGCAACAGCTCCAGGTGAATGA
GTTGATGAACATCACTCAGGTCAACATGGACAAGGCGGTAGAAAGAGATCAGAAACTCCCTGAGCTGGATGACTATGCAG
ATGGGTGGCAGGCAGGACAGTCCCAGTTTGAAACAAGCACTGCCAAGCTGTAGAGTAAAAATTGGTGGAAGAATTGCAAG
ATATGGGCAACTGAGATTAGCATTGTGCTTATTGTCACCACCATCATC

Alignment

ORF - retro_pcap_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 92.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAGAPAGSSAASGSNRRLQQTQNQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKL
          S..A...S...S.SN.RLQQ.Q.QV.E...I..VN.DK..ERDQKL.ELDD.AD..QAG.SQFETS.AKL
Retrocopy SLAAISFSRLISSSNQRLQQQQLQVNELMNITQVNMDKAVERDQKLPELDDYADGWQAGQSQFETSTAKL

Parental  KRKYWWKNCKMWAIGIGVLVIIIIII
          ..K.WWKNCK.WA..I....I...II
Retrocopy *SKNWWKNCKIWATEISIVLIVTTII

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_389 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005770	1 retrocopy	retro_mdom_273,
Mus musculus	ENSMUSG00000028955	1 retrocopy	retro_mmus_1851,
Otolemur garnettii	ENSOGAG00000009797	1 retrocopy	retro_ogar_2300,
Procavia capensis	ENSPCAG00000004825	1 retrocopy	retro_pcap_389 ,
Tarsius syrichta	ENSTSYG00000007733	6 retrocopies	retro_tsyr_1027, retro_tsyr_1435, retro_tsyr_1634, retro_tsyr_1757, retro_tsyr_524, retro_tsyr_968,